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revision 1.40, Wed Oct 12 03:12:24 2005 UTC revision 1.41, Tue Oct 18 02:24:23 2005 UTC
# Line 610  Line 610 
610          if ($prevContig eq $contigID && $dir eq $prevDir) {          if ($prevContig eq $contigID && $dir eq $prevDir) {
611              # Here the new segment is in the same direction on the same contig. Insure the              # Here the new segment is in the same direction on the same contig. Insure the
612              # new segment's beginning is next to the old segment's end.              # new segment's beginning is next to the old segment's end.
613              if (($dir eq "-" && $beg == $prevBeg - $prevLen) ||              if ($dir eq "-" && $beg + $len == $prevBeg) {
614                  ($dir eq "+" && $beg == $prevBeg + $prevLen)) {                  # Here we're merging two backward blocks, so we keep the new begin point
615                  # Here we need to merge two segments. Adjust the beginning and length values                  # and adjust the length.
616                  # to include both segments.                  $len += $prevLen;
617                    # Pop the old segment off. The new one will replace it later.
618                    pop @retVal;
619                } elsif ($dir eq "+" && $beg == $prevBeg + $prevLen) {
620                    # Here we need to merge two forward blocks. Adjust the beginning and
621                    # length values to include both segments.
622                  $beg = $prevBeg;                  $beg = $prevBeg;
623                  $len += $prevLen;                  $len += $prevLen;
624                  # Pop the old segment off. The new one will replace it later.                  # Pop the old segment off. The new one will replace it later.

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